2. Installation¶

Prerequisites

shell (bash, csh, etc, if running on Windows, use a linux container)
python3 >= python3.6
pip3
wget
build tools (make, C/C++ compiler)
(OPTIONAL) docker (required for Module 4: Run a Real Simulation)
(OPTIONAL) file editor for docker config file editing

Estimated time

20 minutes

You will learn

How to install merlin in a virtual environment using pip.
How to install a container platform eg. singularity, docker, or podman.
How to configure merlin.
How to test/verify the installation.

This section details the steps necessary to install merlin and its dependencies. Merlin will then be configured for the local machine and the configuration will be checked to ensure a proper installation.

2.1. Installing Merlin ¶

A merlin installation is required for the subsequent modules of this tutorial.

Once merlin is installed, it requires servers to operate. While you are able to host your own servers, we will use merlin’s containerized servers in this tutorial. However, if you prefer to host your own servers you can host a redis server that is accessible to your current machine. Your computer/organization may already have a redis server available you can use, please check with your local system administrator.

Create a virtualenv using python3 to install merlin.

python3 -m venv --prompt merlin merlin_venv

Activate the virtualenv.

source merlin_venv/bin/activate
or
source merlin_venv/bin/activate.csh

The (merlin) <shell prompt> will appear after activating.

You should upgrade pip and setuptools before proceeding.

pip3 install setuptools pip -U

Install merlin through pip.

pip3 install merlin

Check to make sure merlin installed correctly.

which merlin

You should see that it was installed in your virtualenv, like so:

~/<path_to_virtualenv>/merlin_venv/bin/merlin

If this is not the output you see, you may need to restart your virtualenv and try again.

When you are done with the virtualenv you can deactivate it using deactivate, but leave the virtualenv activated for the subsequent steps.

deactivate

2.1.1. Redis Server ¶

A redis server is required for the celery results backend server, this same server can also be used for the celery broker. We will be using merlin’s containerized server however we will need to download one of the supported container platforms avaliable. For the purpose of this tutorial we will be using singularity.

# Update and install singularity dependencies
apt-get update && apt-get install -y \
  build-essential \
  libssl-dev \
  uuid-dev \
  libgpgme11-dev \
  squashfs-tools \
  libseccomp-dev \
  pkg-config

# Download dependency go
wget https://go.dev/dl/go1.18.1.linux-amd64.tar.gz

# Extract go into local
tar -C /usr/local -xzf go1.18.1.linux-amd64.tar.gz

# Remove go tar file
rm go1.18.1.linux-amd64.tar.gz

# Update PATH to include go
export PATH=$PATH:/usr/local/go/bin

# Download singularity
wget https://github.com/sylabs/singularity/releases/download/v3.9.9/singularity-ce-3.9.9.tar.gz

# Extract singularity
tar -xzf singularity-ce-3.9.9.tar.gz

# Configure and install singularity
cd singularity-ce-3.9.9
./mconfig && \
  make -C ./builddir && \
  sudo make -C ./builddir install

2.2. Configuring Merlin ¶

Merlin requires a configuration script for the celery interface. Run this configuration method to create the app.yaml configuration file.

merlin config --broker redis

The merlin config command above will create a file called app.yaml in the ~/.merlin directory. If you are running a redis server locally then you are all set, look in the ~/.merlin/app.yaml file to see the configuration, it should look like the configuration below.

broker:
    name: redis
    server: localhost
    port: 6379
    db_num: 0

results_backend:
    name: redis
    server: localhost
    port: 6379
    db_num: 0

More detailed information on configuring Merlin can be found in the configuration section.

2.3. Checking/Verifying Installation ¶

First launch the merlin server containers by using the merlin server commands

merlin server init
merlin server start

A subdirectory called merlin_server/ will have been created in the current run directory. This contains all of the proper configuration for the server containers merlin creates. Configuration can be done through the merlin server config command, however users have the flexibility to edit the files directly in the directory. Additionally an preconfigured app.yaml file has been created in the merlin_server/ subdirectory to utilize the merlin server containers . To use it locally simply copy it to the run directory with a cp command.

cp ./merlin_server/app.yaml .

You can also make this server container your main server configuration by replacing the one located in your home directory. Make sure you make back-ups of your current app.yaml file in case you want to use your previous configurations. Note: since merlin servers are created locally on your run directory you are allowed to create multiple instances of merlin server with their unique configurations for different studies. Simply create different directories for each study and run merlin server init in each directory to create an instance for each.

mv ~/.merlin/app.yaml ~/.merlin/app.yaml.bak
cp ./merlin_server/app.yaml ~/.merlin/

The merlin info command will check that the configuration file is installed correctly, display the server configuration strings, and check server access.

merlin info

If everything is set up correctly, you should see:

.
.
.

Merlin Configuration
-------------------------

 config_file        | <user home>/.merlin/app.yaml
 is_debug           | False
 merlin_home        | <user home>/.merlin
 merlin_home_exists | True
 broker server      | redis://localhost:6379/0
 results server     | redis://localhost:6379/0


Checking server connections:
----------------------------
broker server connection: OK
results server connection: OK

Python Configuration
-------------------------
.
.
.

2.4. (OPTIONAL) Docker Advanced Installation ¶

2.4.1. RabbitMQ Server ¶

This optional section details the setup of a rabbitmq server for merlin. A rabbitmq server can be started to provide the broker, the redis server will still be required for the backend. Merlin is configured to use ssl encryption for all communication with the rabbitmq server. An ssl server requires ssl certificates to encrypt the communication through the python ssl module python ssl . This tutorial can use self-signed certificates created by the user for use in the rabbitmq server. The rabbitmq server uses Transport Layer Security (TLS) (often known as “Secure Sockets Layer”). Information on rabbitmq with TLS can be found here: rabbit TLS

A set of self-signed keys is created through the tls-gen package. These keys are then copied to a common directory for use in the rabbitmq server and python.

git clone https://github.com/michaelklishin/tls-gen.git
cd tls-gen/basic
make CN=my-rabbit CLIENT_ALT_NAME=my-rabbit SERVER_ALT_NAME=my-rabbit
make verify
mkdir -p ${HOME}/merlinu/cert_rabbitmq
cp result/* ${HOME}/merlinu/cert_rabbitmq

The rabbitmq docker service can be added to the previous docker-compose.yml file.

version: '3'

networks:
  mernet:
    driver: bridge

services:
  redis:
    image: 'redis:latest'
    container_name: my-redis
    ports:
      - "6379:6379"
    networks:
      - mernet

  rabbitmq:
    image: rabbitmq:3-management
    container_name: my-rabbit
    tty: true
    ports:
      - "15672:15672"
      - "15671:15671"
      - "5672:5672"
      - "5671:5671"
    environment:
      - RABBITMQ_SSL_CACERTFILE=/cert_rabbitmq/ca_certificate.pem
      - RABBITMQ_SSL_KEYFILE=/cert_rabbitmq/server_key.pem
      - RABBITMQ_SSL_CERTFILE=/cert_rabbitmq/server_certificate.pem
      - RABBITMQ_SSL_VERIFY=verify_none
      - RABBITMQ_SSL_FAIL_IF_NO_PEER_CERT=false
      - RABBITMQ_DEFAULT_USER=merlinu
      - RABBITMQ_DEFAULT_VHOST=/merlinu
      - RABBITMQ_DEFAULT_PASS=guest
    volumes:
      - ~/merlinu/cert_rabbitmq:/cert_rabbitmq
    networks:
      - mernet

  merlin:
    image: 'llnl/merlin'
    container_name: my-merlin
    tty: true
    volumes:
      - ~/merlinu/:/home/merlinu
    networks:
      - mernet

When running the rabbitmq broker server, the config can be created with the default merlin config command. If you have already run the previous command then remove the ~/.merlin/app.yaml or ~/merlinu/.merlin/app.yaml file , and run the merlin config command again.

merlin config

The app.yaml file will need to be edited to add the rabbitmq settings in the broker section of the app.yaml file. The server: should be changed to my-rabbit. The rabbitmq server will be accessed on the default TLS port, 5671.

broker:
    name: rabbitmq
    server: my-rabbit
    password: ~/.merlin/rabbit.pass

results_backend:
    name: redis
    server: my-redis
    port: 6379
    db_num: 0

To complete the config create a file ~/merlinu/.merlin/rabbit.pass and add the password guest.

The aliases defined previously can be used with this set of docker containers.

2.4.2. Redis TLS Server ¶

This optional section details the setup of a redis server with TLS for merlin. The reddis TLS configuration can be found in the Security with redis section. A newer redis (version 6 or greater) must be used to enable TLS.

A set of self-signed keys is created through the tls-gen package. These keys are then copied to a common directory for use in the redis server and python.

git clone https://github.com/michaelklishin/tls-gen.git
cd tls-gen/basic
make CN=my-redis CLIENT_ALT_NAME=my-redis SERVER_ALT_NAME=my-redis
make verify
mkdir -p ${HOME}/merlinu/cert_redis
cp result/* ${HOME}/merlinu/cert_redis

The configuration below does not use client verification --tls-auth-clients no so the ssl files do not need to be defined as shown in the Security with redis section.

version: '3'

networks:
  mernet:
    driver: bridge

services:
  redis:
    image: 'redis'
    container_name: my-redis
    command:
      - --port 0
      - --tls-port 6379
      - --tls-ca-cert-file /cert_redis/ca_certificate.pem
      - --tls-key-file /cert_redis/server_key.pem
      - --tls-cert-file /cert_redis/server_certificate.pem
      - --tls-auth-clients no
    ports:
      - "6379:6379"
    volumes:
      - "~/merlinu/cert_redis:/cert_redis"
    networks:
      - mernet

  rabbitmq:
    image: rabbitmq:3-management
    container_name: my-rabbit
    tty: true
    ports:
      - "15672:15672"
      - "15671:15671"
      - "5672:5672"
      - "5671:5671"
    volumes:
      - "~/merlinu/rabbbitmq.conf:/etc/rabbitmq/rabbitmq.conf"
      - "~/merlinu/cert_rabbitmq:/cert_rambbitmq"
    networks:
      - mernet

The rabbitmq.conf file contains the configuration, including ssl, for the rabbitmq server.

default_vhost = /merlinu
default_user = merlinu
default_pass = guest
listeners.ssl.default = 5671
ssl.options.ccertfile = /cert_rabbitmq/ca_certificate.pem
ssl.options.certfile = /cert_rabbitmq/server_certificate.pem
ssl.options.keyfile = /cert_rabbitmq/server_key.pem
ssl.options.verify = verify_none
ssl.options.fail_if_no_peer_cert = false

Once this docker-compose file is run, the merlin app.yaml file is changed to use the redis TLS server rediss instead of redis.

Merlin

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